Supplementary material to Table 3 of the article

The role of PR 10 proteins and molecular components of moulds and yeast in atopic dermatitis patients, J. Čelakovská, R. Vaňková, H. Skalská, J. Krejsek & C. Andrýs

Links to the interactive graph and tables:

Top 8rules by Fisher Exact test

Top 50rules by lift

Top 97 rules min support 10

 

Explanation in Brief:

The sensitization of specific IgE components (molecular components of PR 10 proteins, mould and yeast), obtained with ALEX2 Allergy Explorer, was compared at different levels of atopic dermatitis (AD).

The sets of associated positive allergens reagents are presented (semiquantitative levels of measurement IgE > 0.3).

Significant sets of molecular components associated in pairs and triplets were in the relation to the severity of atopic dermatitis, the occurrence of asthma bronchial, and allergic rhinitis.

We used the association rules method with the interest to study the most frequent sets of simultaneously positive allergen reagents (PR 10 proteins and molecular components of moulds and yeast) observed in a patient in coincidence with allergic dermatitis.

Packages arules, arulesViz  (Hahsler, 2017, 2021; Hahsler et al., 2005; Webb, 2007) and several related R packages were used to specify sets of associated components, and to present complementary characteristics in interactive graphs and tables.

The interactive plot and tables present sets of associated components and complementary characteristics of a set (rule).

Association Rules:

The association rules X→Y, where X on the left-hand side (LHS) represents items (allergens, AB, or AR). Y on the right-hand side (RHS) represents AD. The length of the set on the LHS can vary from 1 to a specified limit. Setting the maximal length of rule 5 detects sets up to 5 associated reagents at any LHS. In addition, a minimum threshold of 0.1 (corresponds to frequency 10 in our data) was set up as support (frequency) of the rules which satisfied the limits on length.

Support of a rule decreases with the increasing length of the rule.

The confidence of the rule X→Y corresponds to the conditional probability P(Y/X) and estimates the probability of AD presented on RHS knowing that corresponding subset X of allergen reagents on LHS is observed. The maximum value of confidence equals one.

Lift (the measure of interestingness) equals support(X, Y)/(support(X) . support (Y)). The value measures the deviation of the support of the rule from the support expected under independence (under independence X, Y, lift = 1). Lift values >> 1 indicate stronger associations. The measure is sensitive to small values in the denominator (when support is close to 0).

 

Vizualizations

Static look (details available in the interactive plot) presents rules with significant associations (the significance level p, Fisher’s Exact Test).

Lift and confidence estimate the predictive quality, support describes the relative frequency of the rule in the data set (n = 100), and the order means the number of components of the rule. Circle diameters are proportional to the support of a rule.

The presented set of 8 rules with a significance level p < 0.01 presents an overall false discovery rate of 0.05 (Holm adjustment).

 

:

Figure 1: Static look at the details of the selected rule in the interactive graph. Top 8rules by Fisher Exact test

Circle diameters are proportional to the support (relative frequency based on total n = 100 patients). Characteristics of a rule are visible after approaching the mouse pointer to the circle. The upper left part allows the selection of a component of the plot.

Statistical analysis in more detail is described in the article [1], Table 3 and Table 4.

 

Figure 2: Static look to the interactive table with selection to show 10 entries.
Top 50rules by lift
Symbols ∆
allow to sort (in the interactive mode) rows in ascending or descending order on the selected column. In this view, data is sorted in descending order by confidence.

 

Link to the interactive table Top 97 rules min support 10

 

References

1.       Čelakovská J., Vaňková R., Skalská H., Krejsek J. & Andrýs C.: The role of PR 10 proteins and molecular components of moulds and yeast in atopic dermatitis patients. Food and Agricultural Immunology, 33(1), 780-798, https://www.tandfonline.com/doi/full/10.1080/09540105.2022.2130183

2.       Hahsler M (2021). arulesViz: Visualizing Association Rules and Frequent Itemsets. R package version 1.5-1, https://CRAN.R-project.org/package=arulesViz.

3.       Hahsler M (2017). “arulesViz: Interactive Visualization of Association Rules with R.R Journal, 9(2), 163–175. ISSN 2073-4859

4.       Hahsler, M., Grün, B., Hornik, K., & Buchta, C. (2005). Introduction to arules – A computational environment for mining association rules and frequent item sets. Journal of Statistical Software, 14(15), http://www.jstatsoft.org/. https://doi.org/10.18637/jss.v014.i15 

5.       Webb, G. I. (2007). Discovering significant patterns. Machine Learning, 68(1), 1–33. https://doi.org/10.1007/s10994-007-5006-x. 

 

https://www.tandfonline.com/doi/full/10.1080/09540105.2022.2130183

https://doi.org/10.1080/09540105.2022.2130183